In Illinois, the route has a total length of 140.82 miles (226.63 km).[3] In Wisconsin, I-39 has a distance of 182 miles (293 km). With the exception of an eight-mile (13 km) segment around Portage, the Interstate shares a route with at least one other route number in the state. From Rockford to Portage, I-39 is concurrent with I-90. I-94 joins the pair in Madison until Portage. At 29 miles (47 km) in length, this concurrency of three Interstates is the longest in the country. From Portage northward, US 51 is co-signed with the Interstate and has exit numbers based on its mileage.

For all but 1 mile (2 km) that Interstate 39 is in Illinois, it is designated concurrently with U.S. Route 51. The southern terminus of I-39 is less than 1 mile (2 km) from Interstate 74 as it runs around Normal.

I-39 enters from Illinois along with I-90, passing under Stateline Road, and bypasses Beloit to the east. East of the town, the route has a cloverleaf interchange that serves as the terminus for both WIS 81—which heads westward into Beloit—and I-43, which provides access to Milwaukee. The I-39/90 concurrency continues to the north and is joined by WIS 11 about 7 mi (11 km) north of the I-43 interchange. The route bypasses Janesville to the east, although interchanges with US 14 (where WIS 81 leaves the concurrency) and WIS 26 provide access to the town. The route continues generally to the north, crossing the Rock River before having an interchange with WIS 59 that provides access to Edgerton to the west.[5] Subsequently, the route enters Dane County as it passes west of Lake Koshkonong. It is joined by US 51 and serves as the southern terminus of WIS 73. US 51 leaves the route 4 mi (6 km) to the north, about 7 mi (11 km) east of Stoughton. The Interstate gradually turns westward around Utica to an interchange with CTH N. It then turns gradually back to the north and interchanges with US 12 and US 18 in Madison. I-39 and I-90 bypass Madison to the east, and I-94 joins the concurrency at the eastern terminus of WIS 30, an interchange known as the Badger Interchange.[6] About 2 mi (3 km) to the north, the highway crosses US 151, which includes a south-side access to High Crossing Boulevard. The last two Madison area interchanges are US 51 three miles (5 km) northwest of the US 151 interchange and WIS 19 another mile northwest of the US 51 interchange. Access is provided to CTH V just west of DeForest four miles (6 km) further north. I-39/I-90/I-94 enter Columbia County four miles (6 km) north-northwest of CTH V.[7]

The Interstates cross WIS 60 at an interchange three miles (5 km) north of the county line west of Arlington and CTH CS at another interchange four miles (6 km) further north near Poynette. The highway crosses the Wisconsin River four miles (6 km) north of CTH CS. At three miles (5 km) further along the route from the river, I-39 leaves the concurrency with I-90 and I-94 and turns northward while the other two interstates turn northwest. WIS 78 terminates at this interchange and heads southwest. This is the starting point of the segment of freeway that carries the I-39 route alone. The interstate crosses WIS 33, the first of three interchanges accessing Portage, two miles (3 km) north of I-90/I-94. After crossing the Wisconsin River again, I-39 crosses the second interchange—this one with WIS 16 and turns northeast to an interchange with US 51. The US route joins the Interstate and both turn north once again and leave the Portage area and, after four miles (6 km), enter Marquette County.[8]

WIS 23 joins I-39/US 51 northbound, 4 miles (6 km) from the county line. The three highways pass along Buffalo Lake and encounter a south-side half interchange with CTH D in the town of Packwaukee. WIS 23 leave the concurrency to the east at WIS 82 near Oxford. and the freeway takes a due north route to pass Westfield. I-39/US 51 enters Waushara County six miles (10 km) north of Westfield.[9] Four miles north of the county line, I-39 / US 51 junction with WIS 21 in Coloma. I-39/US 51 meet an interchange in Hancock with CTH V five miles (8 km) further north and WIS 73 crosses in Plainfield after another five miles (8 km). This is two miles (3 km) south of the Portage County line.[10] In Portage County, I-39/US 51 takes a straight due north trajectory which provides access to CTH D, CTH W and WIS 54 (also Business U.S. 51) over twelve miles (19 km). The WIS 54 interchange and the CTH B interchange a mile and a half north of it provide access for Plover. The next four interchanges—CTH HH, US 10 Eastbound / WIS 66 Westbound, Stanley Street and Business US 51 provide access to Stevens Point. Amongst these interchanges, the freeway turns northwestward, bypassing the city to the east and north. I-39/US 51 cross two more interchanges while in Portage County: Casimir Road four miles (6 km) northwest of Stevens Point,[11] and Westbound US 10 two miles (3 km) north of Casimir Road. The freeway then parallels the Wisconsin River for six miles (10 km) to an Interchange with CTH DB east of Lake DuBay and one mile (1.6 km) south of the Marathon County line.[12]

WIS 34 terminates at an interchange with I-39/US 51 in Knowlton three miles (5 km) northwest of the freeway's entry into Marathon County. The freeway turns due north from this interchange. WIS 153 crosses the freeway four miles further north in Mosinee. Maple Ridge Road crosses after another two miles (3 km) as the freeway turns northeastward into Kronenwetter.[13] An interchange with Business US 51 is just south of the Wisconsin River crossing after four miles (6 km) from Maple Ridge Road. I-39 ends two miles (3 km) further north at the interchange with WIS 29 East just southwest of Wausau.[14]

Interstate 72 where Interstate 39 was supposed to have an interchange in Decatur

When the Interstate Highway System was first being planned, Illinois made a request for a north–south highway from South Beloit to Salem. The project was deemed a low priority and was shelved. US 51, which ran mostly down the middle of the state, became a heavily traveled two-lane arterial road, experiencing many crashes and earning the nickname "Killer 51".

In the late 1960s and early 1970s, a major supplemental freeway system plan was proposed, with the goal of providing Illinois residents access to freeways within 30 minutes or less. One of the proposed routes, FAP 412, was a route that would extend from US 20 in Rockford to I-57 just north of Salem, similar to the earlier requested route. Due to traffic counts, only the portion between Rockford and Decatur was prioritized.[15]

Over the course of 1970s, planning for the US 51 supplemental freeway (officially known as the North–South Freeway) took place in earnest. However, debate ensured over what type of highway should be built. IDOT wanted the entire highway built to Interstate standards, but a transportation committee established to review the proposed supplemental freeway system recommended only Interstate/freeway construction between Rockford and I-80.[16] The highway from Oglesby south to Decatur was recommended to be a four-lane divided expressway, utilizing the existing road where possible. After a decade of lobbying and back and forth debate, Governor James R. Thompson announced in 1986 that US 51 would be rebuilt to Interstate standards from Oglesby to Bloomington–Normal.[17]

Mainly due to funding concerns, it was decided that US 51 would not built to Interstate standards between Bloomington-Normal and Decatur.[18] That segment was instead upgraded to a four-lane divided expressway, with mostly at-grade intersections, just like what was proposed by the transportation committee. To this day, there remains ramp stubs northwest of the city along I-72, where the highways were to connect.[19] There are no present plans to extend I-39 to connect at this unbuilt interchange.

The first segment of the freeway opened 1984 from IL 5 (now I-88) in Rochelle, to US 20 in Rockford.[20] When the freeway was completed south from IL 5 to I-80 in 1986, IDOT officially requested an Interstate designation for the new highway, and I-39 was officially designated.[21]

By December 1987, construction on the section of I-39 between I-80 and IL 251 was finished. The next section, between IL 251 and I-55 in Bloomington-Normal, was completed by 1992, although this stretch of the highway was opened in several phases as completed.[22] In December 1989, the section from Bloomington–Normal to Hudson opened, a distance of about 4.4 miles (7.1 km)[23] In early September 1992, another segment opened from IL 116 north to IL 17.[24]

In Wisconsin, the highway was officially designated in 1992.[25] In October 1993, AASHTO established part of I-39 in its northern section between Rockford and Rib Mountain, Wisconsin, then designated I-39 along existing portions of I-90, I-94, and US 51. However, this part of the highway was not marked as I-39 for another four years, primarily because the Wisconsin Highway Department had to reconstruct the interchange connecting I-90 and I-94 with WIS 78 near Portage.[26] Signs denoting I-39 were placed along the highway in Wisconsin until 1996, when the section between Portage and Rib Mountain, Wisconsin (near Wausau) received its signs.[25] This occurred after then Governor Tommy Thompson designated the stretch between Portage and Wausau in 1996 after a five-year push to get the Interstate designation approved.[26] The remaining segment along I-90/I-94 was not signed for I-39 until late 1998[25] The section between the I-90/I-94 interchange and US 51's interchange in Portage was previously a part of WIS 78. That route was truncated back to its current terminus when the Interstate's designation went into effect.[27] The designation of I-39 violated Wisconsin's rule of not having any state trunk highway number duplicated—Interstate, US or state—as WIS 39 already existed.[25]

The Illinois Department of Transportation is in the preliminary design stages for a project involving reconstruction of I-39 from US 20 east to Harrison Avenue in Rockford. The goal of the project is to reconstruct ramps to modern-day standards, reconstruct and widen I-39 to six lanes between the US 20 and I-90 interchanges, and allow southbound I-39 traffic to use through lanes at the US 20 interchange.[28] Currently, southbound I-39 traffic must exit from the US 20 freeway on a single lane ramp.